Identification of drug resistance mutations in HIV from constraints on natural evolution

Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions, inferred from sequence data obtained prior to the use of antiretroviral drugs, can be used to identify clinically significant sites of resistance mutations. Successful predictions of the resistance sites indicate progress in the development of successful models of real viral evolution at the single residue level, and suggest that our approach may be applied to help design new therapies that are less prone to failure even where resistance data is not yet available.Comment: 5 pages, 3 figure

For T Cell Receptors, Some Breakups Might Not Last Forever

Does the affinity or half-life of peptide-MHC-T cell receptor (TCR) interactions determine T cell activation? In this issue of Immunity, Aleksic et al. (2010) propose a role for the on rate through multiple rebindings to the same TCR

Tripartite entanglement detection through tripartite quantum steering in one-sided and two-sided device-independent scenarios

In the present work, we study tripartite quantum steering of quantum correlations arising from two local dichotomic measurements on each side in the two types of partially device-independent scenarios: $1$-sided device-independent scenario where one of the parties performs untrusted measurements while the other two parties perform trusted measurements and $2$-sided device-independent scenario where one of the parties performs trusted measurements while the other two parties perform untrusted measurements. We demonstrate that tripartite steering in the $2$-sided device-independent scenario is weaker than tripartite steering in the $1$-sided device-independent scenario by using two families of quantum correlations. That is these two families of quantum correlations in the $2$-sided device-independent framework detect tripartite entanglement through tripartite steering for a larger region than that in the $1$-sided device-independent framework. It is shown that tripartite steering in the $2$-sided device-independent scenario implies the presence of genuine tripartite entanglement of $2\times 2 \times 2$ quantum system, even if the correlation does not exhibit genuine nonlocality or genuine steering.Comment: 14 pages, 4 figures, accepted for publication in Physical Review

An Effective Membrane Model of the Immunological Synapse

The immunological synapse is a patterned collection of different types of receptors and ligands that forms in the intercellular junction between T Cells and antigen presenting cells (APCs) during recognition. The synapse is implicated in information transfer between cells, and is characterized by different spatial patterns of receptors at different stages in the life cycle of T cells. We obtain a minimalist model that captures this experimentally observed phenomenology. A functional RG analysis provides further insights.Comment: 6 pages, 3 figures, submitted for publicatio

Reduction of gas bubbles and improved critical current density in Bi-2212 round wire by swaging

Bi-2212 round wire is made by the powder-in-tube technique. An unavoidable property of powder-in-tube conductors is that there is about 30% void space in the as-drawn wire. We have recently shown that the gas present in the as-drawn Bi-2212 wire agglomerates into large bubbles and that they are presently the most deleterious current limiting mechanism. By densifying short 2212 wires before reaction through cold isostatic pressing (CIPping), the void space was almost removed and the gas bubble density was reduced significantly, resulting in a doubled engineering critical current density (JE) of 810 A/mm2 at 5 T, 4.2 K. Here we report on densifying Bi-2212 wire by swaging, which increased JE (4.2 K, 5 T) from 486 A/mm2 for as-drawn wire to 808 A/mm2 for swaged wire. This result further confirms that enhancing the filament packing density is of great importance for making major JE improvement in this round-wire magnet conductor.Comment: To be published in IEEE Transactions on Applied Superconductivity, 23, xxxxxx (2013